[Biojava-l] JPAT API

[Matthew Pocock]

Mike,

This looks like fun code. It would be great if we could make the biojava
code a good starting point for this type of project. Do you have any views
about our code base and what makes it attractive or unattractive for
developing something like jpat? I want to get clear in my head how your code
plugs together so here are some (possibly stupid) questions.

You seem to be passing arround proteins as Strings. Was there a reason for
this, given that you use a concept of Residue within the package?

Your residue objects encapsulate the information about a single ammino acid.
This is analogus to our Residue objects. I think we would store some of the
information like masses in an annotation bundle or in a residue-lookup
table, but that is implementation detail.

Peptides seem to look like our Features - they specify a region within a
parent sequence that has some additional meaning.

PepTools seems to be living multiple lives. It supplys realy useful
constants, and formatting. It is the analogue of our Alphabet objects,
complete with an exception throwing function.  It also is the base class for
things that process proteins, either into arrays of peptides, or just
returning summary statistics. I guess the peptide makers are like the
Annotator interface which adds features to a sequence using some algorithm.

The Protease and Digest classes confuse me a bit. Is there some table of all
known proteases loaded somewhere in memory? I guess these are the static
final String fields in Protease. Why did you go for protease labels rather
than protease objects? I am assuming that Digest.getPeptides behaves
differently depending on what protease you use, in which case a Protease
object with methods that parameterise the search algorithm in Digest would
seem logical.

Thanks again for posting the URL. It is great to look at somebody elses
ideas. Could you just tell us a bit about the license for use of the library
and for the source code?

Matthew

"Jones, Mike" wrote:

> jpat - Contains utilities for performing protein digestion, fragment-ion
> prediction, mass calculations and mass or sequence searching.
> Some of you might find it interesting and I would love to get some
> feedback on it. You can find it at http://www.pixelgate.net/mjones/
> Mike
>
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